address comments

sub-packages/bionemo-noodles/src/bionemo/noodles/nvfaidx.py

@@ -40,6 +40,7 @@ def __init__(self, reader: PyIndexedMmapFastaReader, seqid: str, length: int) ->
             - out of bounds indexing is truncated: query[1:999999999] will return a string from position 1 to the terminus.
             - reversed slices return the empty string: query[999:1] is the empty string.
             - empty slice returns the full string: query[:] is the full string of the sequence.
+            - beginning of slice is beyond the range of the contig, the empty string is returned.
 
         Additionally there are convenience methods that you may find useful in the class definition.
 
@@ -178,18 +179,6 @@ def __init__(self, fasta_path: str | Path, faidx_path: Optional[str | Path] = No
                 raise ValueError("unreachable condition.")
 
         self.records: Dict[str, PyFaidxRecord] = {record.name: record for record in self.reader.records()}
-        return
-        if ignore_existing_fai:
-            self.reader = PyIndexedMmapFastaReader(fasta_path, ignore_existing_fai=ignore_existing_fai)
-        elif faidx_path is not None:
-            self.reader = PyIndexedMmapFastaReader.from_fasta_and_faidx(fasta_path, faidx_path)
-        else:
-            # No faidx path is passed, ignore_existing is always False in this branch
-            #   if the faidx exists, we use it
-            #   if the faidx does not exist, we dont.
-            self.reader = PyIndexedMmapFastaReader(fasta_path, ignore_existing_fai=ignore_existing_fai)
-
-        self.records: Dict[str, PyFaidxRecord] = {record.name: record for record in self.reader.records()}
 
     def __getitem__(self, seqid: str) -> SequenceAccessor:  # noqa: D105
         if seqid not in self.records:

sub-packages/bionemo-noodles/tests/bionemo/noodles/test_nvfaidx.py

@@ -263,6 +263,8 @@ def _test_faidx_generic(faidx_obj):
     # Should see this is out of bounds and return empty or throw an error
     assert index["chr4"][17:17] == ""
 
+    assert index["chr4"][17:] == ""
+
 
 def test_nvfaidx_python_interface(sample_fasta):
     nvfaidx_index = NvFaidx(sample_fasta)